Differentiating mechanism from outcome for ancestry-assortative mating in admixed human populations

Population genetic theory, and the empirical methods built upon it, often assume that individuals pair randomly for reproduction. However, natural populations frequently violate this assumption, which may potentially confound genome-wide association studies, selection scans, and demographic inference. Within several recently admixed human populations, empirical genetic studies have reported a correlation in global ancestry proportion between spouses, referred to as ancestry-assortative mating. Here, we use forward genomic simulations to link correlations in ancestry between mates to the underlying mechanistic mate-choice process. We consider the impacts of two types of mate-choice model, using either ancestry-based preferences or social groups as the basis for mate pairing. We find that multiple mate-choice models can produce the same correlations in ancestry proportion between spouses; however, we also highlight alternative analytic approaches and circumstances in which these models may be distinguished. With this work, we seek to highlight potential pitfalls when interpreting correlations in empirical data as evidence for a particular model of human mating practices, as well as to offer suggestions toward development of new best practices for analysis of human ancestry-assortative mating.


Figure S2 .
Figure S2.Under the sta5onary-preference model, variance in ancestry within the popula5on decreases as admixture proceeds.The distribu5on of ancestry propor5on is ploGed for the first 20 genera5ons post-admixture for  = 5.

Figure S3 .
Figure S3.Under the increasing-preference model, variance in ancestry within the popula5on decreases as admixture proceeds.The distribu5on of ancestry propor5on is ploGed for the first 20 genera5ons post-admixture for  = 5.To compensate for the decreased variance over 5me, the mate-choice parameter is scaled by the genera5on-specific variance  " # , meaning that the ra5o of () / () increases over 5me (see FigureS1B).

Figure S4 .
Figure S4.Under the broad-preference model, variance in ancestry within the popula5on decreases as admixture proceeds.The distribu5on of ancestry propor5on is ploGed for the first 20 genera5ons post-admixture for  = 5.

Figure S5 .
Figure S5.Under the social group model, variance in ancestry within the popula5on decreases as admixture proceeds.The distribu5on of ancestry propor5on is ploGed for the first 20 genera5ons post-admixture for  = 5.

Figure S6 .
Figure S6.Correla5on in ancestry between mates was not constant over 5me and decayed to near-zero in some simula5ons.For each model, higher values of  produced greater correla5on in ancestry between mates in the early genera5ons.In simula5ons under the sta5onary-preference and broad-preference models, the correla5on in ancestry between mates was near-zero 20 genera5ons post-admixture for  ≤ 10.The same random-ma5ng simula5ons ( = 1; gray) are reproduced in each subplot for reference.Compare to Figure 2.

Figure S7 .
Figure S7.On longer 5me scales, the decay in correla5on between mates differed between the increasingpreference and social groups models.(A) Correla5on between mates reached a stable non-zero plateau maintained over 50 genera5ons post-admixture under the increasing-preference model, for all .(B) While correla5ons between mates were maintained for the first 20 genera5ons post-admixture under the social group model (Figure2), they decayed to zero on longer 5me scales.

Figure S8 .
Figure S8.Under the sta5onary-preference model, a correla5on in ancestry between mates was only observed at genera5on 20 when mate-choice bias was strong enough to largely prevent admixture ( > 10).Each subplot displays the distribu5on of ancestry propor5on at genera5on 20 for the indicated value of .

Figure S9 .
Figure S9.Under the broad-preference model, a correla5on in ancestry between mates was only observed at genera5on 20 when mate-choice bias was strong enough to largely prevent admixture ( > 10).Each subplot displays the distribu5on of ancestry propor5on at genera5on 20 for the indicated value of .

Figure S10 .
Figure S10.Differences in ancestry propor5on between social groups became smaller over 5me, in simula5ons under the social group model.Despite increasing overlap in the distribu5ons, correla5on in ancestry between mates persisted 20 genera5ons post-admixture.A representa5ve example simula5on is shown for  = 5.

Figure S11 .
Figure S11.The transi5on from bimodal distribu5on of ancestry propor5on to unimodal distribu5on was delayed in the social group model (B, D, F, H) rela5ve to the increasing-preference model (A, C, E, G) for the same genera5on and .Four representa5ve examples are shown.

Figure S12 .
Figure S12.The distribu5on of ancestry propor5on was unimodal 20 genera5ons post-admixture in simula5ons under the increasing-preference model (A, C, E) and remained bimodal in simula5ons under the social group model (B, D, F).The bimodality of the distribu5on was more pronounced for larger values of .Three examples are shown, comparing simula5ons with similar correla5on in ancestry between mates at genera5on 20.

Figure S13 .
Figure S13.Differences in ma5ng structure between simula5ons under the increasing-preference (A, C) and social group (B, D) models were more pronounced when the correla5on in ancestry between mates was larger.All individuals in genera5on 20 are shown.Each hexagon represents a bin of 0.025 ancestry propor5on units, colored by density scaled to a maximum value of 1. (A)  = 3 (B)  = 6.(C-D)  = 10.Compare to Figure 3A.

Figure S14 .
Figure S14.Simula5ons under the increasing-preference ( = 5) and social group ( = 7) models produced similar correla5on coefficients with different underlying ma5ng structure.Differences in the underlying structure were difficult to ascertain when visualized as a dot-plot.(A) Correla5on in ancestry propor5on between the two parents of all individuals in genera5on 20.(B) Correla5on in ancestry propor5on between the two parents of a subset of 100 individuals in genera5on 20.

Figure S15 .
Figure S15.Even with a rela5vely small sample size ( = 100), "hexbin" plots can suggest differences between the increasing-preference (A, C) and social group (B, D) models.Differences in the structure of ma5ng pairs is more apparent when the correla5on in ancestry between mates is higher (C, D) .(A)  = 3 (B)  = 6.(C-D)  = 10.Compare to Figure 3C.

Figure S16 .
Figure S16.Correla5on in ancestry propor5on between mates is posi5vely correlated with variance in ancestry propor5on within the popula5on across models and values of .Rela5ve to the other two models, the increasingpreference and social group models maintain a posi5ve correla5on even as variance decreases.Each dot represents one genera5on.

Figure S17 .
Figure S17.Ma5ng can differ significantly from random even when the correla5on in ancestry between mates is very small.(A, B) In simula5ons under the sta5onary-preference model, the correla5on in ancestry between mates was significantly different from 1,000 permuta5ons across all 5me points for  = 10.(C, D) In simula5ons under the broad-preference model, the correla5on between was only significantly different from permuta5on un5l genera5on 10 for  = 10.

Figure S18 .
Figure S18.The difference in ancestry between mates,  # , is an alterna5ve to Pearson correla5on coefficient for measuring the degree to which ma5ng is biased.Representa5ve examples are shown for (A) random ma5ng ( = 1), (B) the increasing-preference model ( = 10), and (C) the social group model ( = 10).Each line represents one individual in genera5on 20, connec5ng the ancestry propor5on of parent 1 and parent 2.

Figure S19 .
Figure S19.Comparison of Δ # to permuta5ons indicates that ma5ng does not always differ from random, even when mate-choice is biased.(A, B) In simula5ons under the sta5onary-preference model, the mean difference in ancestry between mates,  ̅ $%& , was significantly different from the distribu5on of  ̅ '()* for 1,000 permuta5ons across all 5me points for  = 10.(B) In simula5ons under the broad-preference model,  ̅ $%& was only significantly different from the distribu5on of  ̅ '()* for 1,000 permuta5ons un5l around genera5on 10 for  = 10.

Figure S20 .
Figure S20.The rela5onship between the correla5on coefficient for ancestry between mates and expressed ma5ng bias  was similar across models and 5me points.Each dot represents one simula5on.Compare to Figure 5A.

Figure S21 .
Figure S21.Direct comparison of  ̅ $%& between models (instead of the variance-standardized ) demonstrates that for a given correla5on in ancestry between mates, individuals are less similar to their mates under the social group model than under the increasing-preference model.The rela5onship between these variables is not consistent between genera5ons.Each dot represents one simula5on with 5 replicates per .

Figure S22 .
Figure S22.Comparing within each model, larger values of  consistently correspond to longer median localancestry tract lengths.Five replicate simula5ons are shown for each value of .

Figure S23 .
Figure S23.Underes5ma5on of the 5me since admixture is more strongly influenced by earlier genera5ons.In simula5ons under either the increasing-preference or social group model, the discrepancy between the es5mated 5me since admixture and the true 5me since admixture did not increase linearly over 5me, and in some cases appeared to reach a plateau.Each line represents a single simula5on.

Figure S24 .
Figure S24.Underes5ma5on of the 5me since admixture is more strongly influenced by earlier genera5ons Correla5on in ancestry between mates at genera5on 5 more strongly influenced the discrepancy in es5mated 5me since admixture observed at genera5on 20 ( = 0.89) than did the correla5on in ancestry between mates at genera5on 20 ( = 0.46).

Figure S25 .
Figure S25.The effects of con5nuous migra5on differed between mate-choice models.(A, B) Correla5on in ancestry between mates did not differ between simula5ons with and without migra5on, for the sta5onarypreference and broad preference models.(C, D) Under both models with con5nuous migra5on, ma5ng between migrants did not occur more o\en than expected by chance.

Figure S26 .
Figure S26.The effects of con5nuous migra5on differed between mate-choice models.The introduc5on of con5nuous migra5on tended to increase the correla5on between mates under the increasing-preference model, rela5ve to a scenario of pulse-admixture.The opposite trend was observed under the social group model.Correla5on coefficients were generally unaffected by migra5on under the sta5onary-preference and broadpreference models.

Figure S27 .
Figure S27.The disparate impacts of con5nuous migra5on between models were consistent on longer 5me scales.Correla5on between mates with and without con5nuous migra5on is shown under each model for 50 genera5ons post-admixture.